Endogenous viral elements in shrew genomes provide insights into Pestivirus ancient history

Activity: Talk and presentationAcademic presentationAcademic


As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. EVEs are thus genomic fossils to compensate for the absence of physical fossil traces of viruses. Flaviviridae are an important family of viruses, including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. Most EVEs derived from Flaviviridae have been identified in arthropods, but none, to date, in the genome of mammals, even though the family encompasses numerous mammal-infecting members. Through a comprehensive in silico screening of a large dataset of available mammalian genomes, our study identified two novel Flaviviridae-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis), a first in mammals. Homologs of these novel EVEs were subsequently detected in an additional 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of Flaviviridae.
Event titleSMBE Everywhere 2022-23: Global Symposium 5: Evolutionary Genomics of Host-Pathogen Interactions and Antimicrobial Drug Resistance
Event typeConference
OrganiserSociety for Molecular Biology and Evolution (SMBE)
Degree of RecognitionInternational